Quote:
Originally Posted by zenji
When I sign out of Google, I don't expect to lose all my labels (tags/boxes).
When I sign out of the Kindle app, I don't lose anything.
There are countless other examples I could give.
At the very least, a warning would have been nice - indeed, I'd say: basic courtesy.
There is no way I would have signed out if I'd had such a warning.
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Does the word 'collections' or 'shelves' appear at all in this warning?
"Any reading progress, highlights, or notes since your last sync will be lost."
No it doesn't.
Even though I expect for many of us, collections are more important than highlights and notes.
...Just as it also doesn't say that your bookmarks will be retained (and even any words you wrote associated with them).
Indeed, the fact that bookmarks are retained makes me wonder why your collections aren't.
I'm sure someone will leap to the company's defence though** 
I'm very open to some genuine IT expert explaining to me why it's technically impossible or just too massively onerous for the company to retain bookmarks but not collections.
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To people who gave useful advice, thankyou.
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** I notice on forums there's always one or two kind souls who do a better job of defending some company better than any employee ever could. "Well if you don't like the effects Thalidomide have, you can always stop using it! No one forced you to buy a Ford Pinto!" 🤣
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Perhaps if you hadn't made duplicate posts for the same issue, and were capable of taking information given to you in that post and applying it here as well then you wouldn't be so lost.
But since you clearly lack that ability, and did make duplicate posts here let me repeat what was told to you that it might assist you in finally understanding as well help others avoid your blunders in the future.
When you sync your Kobo, it transmits (that's fancy IT talk for sends) certain data to Kobo to store on their servers (servers are like big notebooks to keep information). The information sent includes, but is not limited to:
Collections- the names of any collections you have on the device, in addition to any Kobo purchased books* within those collections.
Bookmarks - any book marks you have in Kobo purchased books*
Annotations - any annotations you have in Kobo purchased books*
*Kobo purchased books which have not been stripped of DRM and sideloaded back to the device.
Information
NOT sent includes the following
ANY INFORMATION ON SIDELOADED BOOKS OR DOCUMENTS TO THE DEVICE
Now as others told you in your other post, it's likely your devices database (a database is fancy IT talk for a means to store information) was corrupted, this would potentially cause the Overdrive issues you had, as well the syncing issues. After all if the information being sent to Kobo is too damaged they can't read it, and your Kobo wont be able to make sense of it when it tries to rebuild. Think of this like trying to build a house from blueprints which have been burned significantly, you might get certain parts right but you'll miss the details of anything on the blueprints which were burned.
TL;DR- Your Kobo's database likely became corrupted which would be the root cause of the issues you had. As literally no one else has had this issue upgrading to a now month+ old firmware. In the future please refrain from making duplicate posts, and perhaps don't make declarative statements when you don't understand what's going on with your device.